StarDist_BF_Neutrophil_dataset

This repository includes a StarDist deep learning model and its training and validation datasets for detecting neutrophils perfused over an endothelial cell monolayer. The model was trained on 36 manually annotated images, achieving an average F1 Score of 0.969. The dataset and model are intended for use in biomedical research, particularly for analyzing interactions between neutrophils and endothelial cells.

Specifications





Model: StarDist for neutrophil detection on endothelial cells




Training Dataset:






Number of Images: 36 paired brightfield microscopy images and label masks




Microscope: Nikon Eclipse Ti2-E, 20x objective




Data Type: Brightfield microscopy images with manually segmented masks




File Format: TIFF (.tif)






Brightfield Images: 16-bit




Masks: 8-bit





Image Size: 1024 x 1022 pixels (Pixel size: 650 nm)





Training Parameters:






Epochs: 400




Patch Size: 992 x 992 pixels




Batch Size: 2





Performance:






Average F1 Score: 0.969




Average IoU: 0.914





Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki)





Reference

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers


Gautier Follain, Sujan Ghimire, Joanna W. Pylvänäinen, Monika Vaitkevičiūtė, Diana Wurzinger, Camilo Guzmán, James RW Conway, Michal Dibus, Sanna Oikari, Kirsi Rilla, Marko Salmi, Johanna Ivaska, Guillaume Jacquemet

bioRxiv 2024.09.30.615654; doi: https://doi.org/10.1101/2024.09.30.615654